Thursday, October 18, 2012

Douglas Axe on Protein Evolution and Magic Numbers

Imagine that I asked you to "prove" evolution by transforming a chimpanzee into a human. Would you recognize the fallacy that I described recently in Why Are Chimps Still Chimps?. Of course you would. Any intelligent person who understands evolution knows that chimps and humans share a common ancestor and both have evolved substantially since the two lineages diverged. In order to change a chimp into a human you would first have to "devolve" it back to the common ancestor and proceed from there. That requires a lot of changes.

Now let's think about two enzymes that are members of the same gene family but have evolved different functions. It's easiest to think of these as two enzymes that are now specific for similar but distinct substrates. Imagine that you were asked to "prove" evolution by changing one of those enzymes into the other? Would you recognize the same fallacy? Would you realize that the most likely evolutionary scenario is that the two different enzyme specificities evolved from an ancestral enzyme that carried out both reactions? [see: The Evolution of Enzymes from Promiscuous Precursors]

Changing one of the modern enzymes into the other would require many changes because in most cases the common ancestor dates back hundreds of millions of years. Many of the changes that have become fixed in the two lineages were not directly involved in selecting one of the substrates over the other (i.e. increasing specificity). They were neutral mutations fixed by random genetic drift after the enzyme became specialized for one or other of the substrates. Many would have to be "reversed" in order to re-create the dual specificity because they would have been detrimental in the ancestral enzyme.

Axe is still hawking the debunked argument he made in his paper last year coauthored with Ann Gauger (link goes to PZ's critique of their paper). Aside from the other failings of the IDiots, the one that damns their enterprise the most is that they will never drop a debunked argument. I can't think of a tactic of theirs that better demonstrates the fact that they start with their conclusion and then reason backwards to find their 'evidence'.

P.S. It looks like the initial word in your last sentence should be "Think" and "his" in the same sentence has an extra vowel.

I've looked at PZ Myers' critique. I don't find it convincing in the least.

First, he uses the same basic argument that Larry is using here. And there is, I believe, a defect in the argument. Why? Because it assumes that 'divergence' has occurred over the whole spectrum of time beginning with all the divergence leading to the initial chimp/human split, and then continuing on until today. But the protein divergence could have occurred in either of those two time periods, or both. Larry assumes 'both.' But there is no reason for knowing this as far as I can see. And the same problem affects Myer's analysis.

Second, his analysis of bridge hands is spurious. Just because the odds of any particular hand are astronomical, this doesn't mean that the odds of any given bridge hand is astronomical. It's not. It's 1.0.

But, if I were to stipulate ahead of time a particular bridge hand, wrote that hand down on paper, and then waited for this particular hand to end up in someone's hands, this would take (and I'll simply accept Myer's calculation) over a million years.

There's a big difference between not specifying a 'hand' ahead of time and not specifying one. And in Axe's paper they were looking for specific mutations, not just any kind of mutation. The calculations would be constructed on a much different basis if any kind of mutation whatsoever would suffice. But that wasn't the case. And it's really rather self-evident.

And in Axe's paper they were looking for specific mutations, not just any kind of mutation. The calculations would be constructed on a much different basis if any kind of mutation whatsoever would suffice.

You have summed up why Axe's assumption is incorrect, and do not pertain to real biological systems.

neo-Darwinists/Darwinists/evolutionary biologists choose to view the situation as you imply; i.e., as if any mutation whatsoever will do. But it is fairly clear, if not self-evident, that 'specific' mutations are needed.

By 'specific' mutations, I don't mean mutations that you know will occur 'beforehand,' because protein domains are so complex that this would be, in general, next to impossible, but I do mean that a particular a.a. at a particular location is required to change. While known only afterwards, nevertheless, they're "specific" vis-a-vis the protein and the organism.

Recently, an experiment was conducted to test for resistance to certain leaf fungus. They looked at very diverse specimens that branched over even 'orders' of plants! And they found the very same a.a. changes at the very same locations along the protein. This is what is meant by 'specific.'

The gene I study (mitochondrial polymerase gamma) encodes a protein that is only 26% identical and ~45% similar between C. elegans and Homo sapiens (ie within Metazoa), yet is does exactly the same job.

So I disagree completely with your assertion. You will find some protein with extreme sequence conservation. But they are actually the minority.

-The Other Jim (embarrassingly, I again forgot to sign my post, this time October 25, 2012 1:11:00 AM. I promise to use the Name/URL function instead of Anonymous...)

It is not possible to make sense of what you said. Not possible to understand what you are asking. It is not subtle. It is not misplaced, it just does not make sense. How would you expect an answer if you write something that can't be understood?

Let me show you:You've delineated two distinct epochs of differentiation: (1) the chimp-human divide, and (2) the subsequent differentiation since this divide.

How the hell is a divide an epoch of differentiation?

Here's two questions: To which of these two periods does this "evolution of distinct functions" pertain? And how would you know?

Two periods? How is the divide a period? How are you thinking of this? Why would it be meaningful where differentiation "happened" and if there were really two "epochs" why should differentiation "pertain" only to one of them?

Obviously there's a lot of garbage going on in your head. You can't make your point clearly. You should not have left school (or should attend a much better one).

Given the lack of clarity I can only expect that you will not even try and clarify what you said, but rather start with my questions without giving any thought to making your "questions" clear. I expect that you will only make it much more of a mess.

This is one of many posts comparing the understanding and interpretation of data on protein functions and evolution by scientists and creationists.

On one side there are thousands of protein chemists, biochemists, molecular biologists, cell biologists, evolutionists and many other scientists studding proteins. The scientists are supported by a huge academic and technical infrastructure worth billions of dollars. On the other side there are a few dozen people, if that, with very limited resources, if any.

In other sectors of life, having a ‘gigantic group’ picking on a ‘little group’ would be considered bullying!

As outstanding as the work of the scientists is, often, their work follows misleading paths, which waist precious resources and, in due course, the well-being and the life of millions of people. This usually happened when misleading dogmas hijack the science. One highly relevant example might be the fields of protein misfolding diseases, including Alzheimer’s, Parkinson’s, Huntington’s, Creutzfeldt-Jakob disease, ALS and many other devastating neurodegenerative diseases.

Unfortunately, the scientists in these fields have departed form one of the most fundamental scientific principles: "Nothing in Biology Makes Sense Except in the Light of Evolution." Interestingly, this principle was enunciated by Theodosius Dobzhansky, who was not only an evolutionary biologist but also a devoted Christian.

There are strong experimental evidence and observations that the ‘protein misfolding concept’ and the ‘prion hypothesis’, which have directed the thinking and the research in these fields for decades, are flawed. Indeed it appears that that the primary proteins implicated in these diseases, including Aβ, tau, α-synuclein, huntingtin, TDP-43 and PrP, are members of the innate immune system and their activity and assembly into oligomers and amyloids are not protein misfolding events or prion activities, as proposed by the protein misfolding concept and the prion hypothesis, but part of their repertoire of immune functions ( http://www.alzforum.org/res/adh/cur/bandea/default.asp; http://precedings.nature.com/documents/3887/version/1). Unlike the ‘prion hypothesis’ and ‘protein misfolding theory’, this new model is fully consistent with and supported by the current experimental data and observations, and it makes biological and evolutionary sense.

Given the medical, public health and economic relevance of these diseases, it would make sense that the scientists, including protein biochemists and evolutionists, would evaluate the pitfalls of the ‘protein misfolding concept’ and the ‘prion hypothesis’, and consider alternative hypotheses. However, that doesn’t seem to be the case. Most scientists respond by being silent, which might be understandable considering that they have spent much, or their entire professional career working under these hypotheses. However, some people who call themselves scientists might even engage in ‘bullying tactics,’ such as derogatory name callings instead of discussing scientific evidence and arguments.

I think ‘indifference’ and ‘bullying’ should not be attributes associated with the field of science or with scientists!

"Unlike the ‘prion hypothesis’ and ‘protein misfolding theory’, this new model is fully consistent with and supported by the current experimental data and observations, and it makes biological and evolutionary sense." If you say "evolutionary sense," it's not exactly clear what you mean. The theory of evolution is four, sometimes six theses bundled up into one, some theses true, others false. 1. species change over time - true, scorpions used to be 8 feet tall 2. species change into other species - I personally believe this though some or many ID advocates don't. However I believe that when a species changes into another the change happens in an archeological blink of an eye, maybe 50,000 years. Many of the major characters that we see in fossils, jaws, eyes, wings, horns, all of them appear suddenly in the fossil record without precursors. 3. common ancestry - I personally believe that the species within phyla are related but the phyla themselves are not related though some or many ID advocates don't. All the major phyla appear roughly simultaneously in the fossil record during the Cambrian Explosion. 4. the strong survive - this is a useless tautology, all it says is those who are effective at reproducing will reproduce 5. all mutations are random - this is false. My theory is that most changes to the genome are directed by the unconscious of the organism itself. Of course a few typos occur due to UV rays from the sun knocking out a DNA molecule here and there but of the 5,000 indels in the human genome in comparison to the chimp genome I argue that they are intentional. So when you say the "misfolding of proteins makes evolutionary sense" it's not even clear what you're asserting.

In my comment above, I stated that the ‘prion hypothesis’ and ‘protein misfolding theory', which have directed the thinking and research in the field of protein misfolding diseases (e.g. Alzheimer’s, Parkinson’s, Huntington’s, Creutzfeldt-Jakob disease and ALS) for decades are misleading. I also stated that unlike these two working hypotheses, the new model on the etiology of these diseases is consistent with and supported by the current experimental data and observations and it makes biological and evolutionary sense.

I think that if you read the two papers (http://www.alzforum.org/res/adh/cur/bandea/default.asp; http://precedings.nature.com/documents/3887/version/1) you’ll understand why I made these statements.

Indeed, the statements are rather bold, and you would think that, if wrong, the thousands of scientists working in these fields, as well as the thousands more studding protein biochemistry and evolution, would present data, observations, or arguments falsifying them.

Becouse of the apparent absence of such evidence or arguments, the researchers in these fields pretend that the problem does not exist. However, as I mention in another comment below, this might be a disservice not only to science, but also to the tens of millions of patients and their families affected by these devastating diseases.

It is somewhat specious to compare the differentiation of the functions of a promiscuous ancestral gene with the split between chimps and humans. In the former, the biochemical functionality has basically become evenly divided whereas, in the latter, one of the evolutionary trajectories has remained largely unchanged while the other has undergone extensive change. The alleged common ancestor of chimps and humans (of which there is still no fossil record) would have looked far more like a chimp than a human. Chimps just haven't been evolving much since the split of 6 million or so years ago.

Huh, what? On what do you base the idea that chimps are "largely" unchanged from a common ancestor and humans not? And how do you know that the ancestor "looked far more" like a chimp than a human? What's the cirteria? And chimps haven't been evolving much since "6 my ago or so" is based on what?

Well, it would help if the fossilized remains of the alleged "common ancestor" of chimps and humans were dug up. But it is generally accepted that the common ancestor of chimps and humans would have looked more like a chimp than a human, just as the common ancestor of monkeys and humans would have looked more like a monkey than a man, or that the common ancestor of mice and men would have looked more like a mouse.

The fossil record for chimps is non-existent save for a few teeth. However, chimpanzees of today are certainly less advanced than the bonobo-like australopiths of 4 million years ago.

Well, it would help if the fossilized remains of the alleged "common ancestor" of chimps and humans were dug up.

Why alleged, and why the quotes? The fossil record being what it is, even if we dig that very species up, how can we be sure beyond reasonable doubt that it's the last straight-line common ancestor? Aren't you demanding too much?

But it is generally accepted that the common ancestor of chimps and humans would have looked more like a chimp than a human,

Generally accepted? Who published such a guess, where, and based on what? How do you propose to quantify "looking like" in an objective way, without an non-anthropocentric bias?

just as the common ancestor of monkeys and humans would have looked more like a monkey than a man,

What does "a monkey" look like? I'm aware of the existence of lots of different simian species. You may think that the common ancestor of, say, the hamadryas baboon and Homo looked more like a baboon than a human, but what if baboons disagree?

or that the common ancestor of mice and men would have looked more like a mouse.

Is it supposed to be a general rule? Let's see if it works:

The last common ancestor of the blue whale and man would have looked more like a blue whale.

The last common ancestor of the domestic sparrow and man would have looked more like a domestic sparrow.

The last common ancestor of the Indian elephant and man would have looked more like an elephant...

"But it is generally accepted that the common ancestor of chimps and humans would have looked more like a chimp than a human, just as the common ancestor of monkeys and humans would have looked more like a monkey than a man, or that the common ancestor of mice and men would have looked more like a mouse."

Nonsense. What's accepted is that features that are common between chimps and humans had to be present in the common ancestor of both. The same for all examples you mentioned.

But I'll wait for your references, since they are so commonly accepted.

"The fossil record for chimps is non-existent save for a few teeth. However, chimpanzees of today are certainly less advanced than the bonobo-like australopiths of 4 million years ago."

Certainly? Whats the criteria for deciding that australopithecus of 4 my ago are more "advanced" than a modern chimp? What do you mean by "advanced"? You're sure you're not confusing "advanced" with "looks more like a human"?

Well, it's simple: ancient hominin fossils are more chimp-like than recent hominins, in a wide range of features. And chimps have lots of "common" ape features, while humans have a lot of "deviations" and oddities. So, it's pretty safe to say that the last chimp/human common ancestor was broadly chimp-like and not human-like. We know that ancestor was quite probably a quadruman with "handy" feet, with a small (chimp-sized) brain, a chimp-like face and skull (look at the australopithecines), chimp-like body fur, chimp-like pelvis, etc. This is no "nonsense", it's just fossil data and Occam's razor.

If you really want to include fossil data, at least the part about chimp-like locomotion and a chimp-like pelvis doesn't hold water. Australopithecines, putative hominins close to the human/chimp LCA (Ardipitecus), and even outliers with preserved pelvises (Oreopithecus) are in that respect very different from chimps, who are knuckle-walking semiquadrupeds while on the ground and suspensory locomotors while in a tree. The specialisations of the modern great apes are just as "odd" as our obligate bipedality.

Perhaps chimpanzees, gorillas and orangutans have convergently evolved some locomotory specializations; that's an interesing hypothesis (three stances of parallel evolution!) that depends on some still controversial reconstructions and interpretations of fossil apes. The chimp pelvis is quite similar to the gorilla pelvis and the orangutan pelvis; it's long-shaped as, in general, ape and monkey pelvises.

The phylogenetic position of Ardipithecus ramidus is also controversial, but the strongest papers place it closer to humans than to chimps. Broadly (and despite all those pictures where it stands upright looking at us with humanized eyes), I find the Ardipithecus skeleton very chimp-like.

It is "alleged" because there is no physical evidence for it in the fossil record at all - no scientist has ever found something that is 5-7 million years old and would fit in with expectations of it. It is only "inferred" rather than "observed" based on DNA similarity. But science is about observations, not inferential speculations.

As we don't have any physical evidence, our best guess is taken from apes that lived close in time to the alleged split, such as the australopiths and ardipiths.They all resemble chimps, bonobos and gorillas far more than they do humans. I think it is safe to say that the alleged common ancestor was a quadruped, had a small brain, had pronounced canines, was covered in fur, had no real nose, had long arms, displayed marked prognathism, had opposable toes and other apish/chimp-like features.

Chimps would basically represent an evolutionary dead-end when compared with the human lineage.

@Pedro: if you want to argue about semantics, let us use the terms "derived" and "primitive". Chimps are primitive in so many ways, and have likely not changed much from their ancestors who lived 4-6 million years ago.

It is "alleged" because there is no physical evidence for it in the fossil record at all - no scientist has ever found something that is 5-7 million years old and would fit in with expectations of it.

There are fossil hominines pretty close to the split (Sahelanthropus, Orrorin), and new ones are being found all the time. Give the paleontologists a few more years and the gaps will be still narrower.

It is only "inferred" rather than "observed" based on DNA similarity. But science is about observations, not inferential speculations.

Science is both about observations and inferences. In a historical science, which is all about reconstructing the past, direct observation is impossible anyway. The fossil record is just one type of evidence, not necessarily privileged (or more "physical" than other types), and any conclusions drawn from it are as inferential as those drawn from molecular analyses. Then, "similarity" doesn't mean much by itself, but shared derived alleles unique to chimps and humans do mean a lot. If we know at least seven identical endogenous retroviruses embedded at the same spots in the genomes of all humans, all chimps and no other species, that's not a mere inference but a solid a proof of shared ancestry.

I don't know of any paleontologist who has proposed that Sahelanthropus Tchadensis(Toumai) or Orronin Tugenensis is even close to being a candidate for the MRCA of humans and chimps. The search continues in much the way as it does for Bigfoot and other mythical beasts.

I would agree with you that fossil evidence can be as much inferential as it is observational, but at least it provides actual physical evidence for the existence of a living organism. DNA evidence,however, can be interpreted in so many more ways because there are so many more factors and possibilities involved.

If all humans and all chimps share certain retroviral sequences, to the exclusion of all other extant species, this could indeed mean shared ancestry, or it could mean direct human descent from chimps, or it could yet mean parallel evolution. Moreover, what happens if it is shown that humans and gorillas share certain ERVs that are not found in chimps?

I don't know of any paleontologist who has proposed that Sahelanthropus Tchadensis(Toumai) or Orronin Tugenensis is even close to being a candidate for the MRCA of humans and chimps.

Quite the opposite. Practically everybody places them both near the split, while of course remaining cautious about the precise status of any fragmentary fossil.

The search continues in much the way as it does for Bigfoot and other mythical beasts.

Except that fossil hominids are real.

I would agree with you that fossil evidence can be as much inferential as it is observational, but at least it provides actual physical evidence for the existence of a living organism. DNA evidence,however, can be interpreted in so many more ways because there are so many more factors and possibilities involved.

Like "it was intelligently designed"?

If all humans and all chimps share certain retroviral sequences, to the exclusion of all other extant species, this could indeed mean shared ancestry, or it could mean direct human descent from chimps,

Excluded on other grounds (chimps are highly derived themselves; they have numerous autapomorphies not shared with humans, including their unique ERV inserts).

or it could yet mean parallel evolution.

Parallel what? numerous identical ERV inserts at the same loci? Do you realise what the probability of that is?

Moreover, what happens if it is shown that humans and gorillas share certain ERVs that are not found in chimps?

Not impossible (after all, chimps might have developed from a subpopulation that happened to lack a particulat ERV), but why discuss a hypothetical situation instead of an acual one? A red herring?

what happens if it is shown that humans and gorillas share certain ERVs that are not found in chimps?

It would mean that there's not been complete resolution. You know about population genetics and the very fact that in evolution populations diverge, thus we should expect some inconsistencies. Right? In other words, while we often describe evolution as if there's only one human, one chimp, and one gorilla, this is not so. Populations carry many more versions of chromosomes than single individuals could. Thus, it is entirely possible to have some pieces (versions of chromosome pieces, alleles) that still exist in both the gorilla population and the human population, but were displaced by other versions (other alleles) in chimps. If we were able to follow each piece of our chromosomes, they might as well coalesce in different individuals in the past. Some farther before the separation among the three populations, some closer to home, and so on.

I hope that was not too obscure. Population genetics; then coalescence theory.

"if you want to argue about semantics, let us use the terms "derived" and "primitive". Chimps are primitive in so many ways, and have likely not changed much from their ancestors who lived 4-6 million years ago."

Semantics are important because they are abused and imparted meanings by creationists that have nothing to do with their usage in biology.

"Chimps" are primitive in the same way that humans are "primitive". They both diverged and kept evolving in different directions since cladogenesis from a common ancestor. According to your logic, a crocodile should be less evolved than a Tyranossaurus because it walks on four legs while a T Rex walked on two. Maybe elephants are more evolved than humans because they have a much more developed nose that they can use to manipulate the environment while we can't?

Are you sure you know anything whatsoever about comparative anatomy to be in a position to judge morphological variability?

And like Piotr pointed out, how do you explain the presence of the SAME endogenous retroviruses in the SAME positions of the genome of chimps and humans without implying that they were already present in a common ancestor?

ERVs have preferential insertion sites. It is not an entirely random process and shared environmental factors may contribute to this. I doubt the probability of such parallel evolution is so great.

I am not raising a red herring about potential shared ERVs in gorillas and humans, but we do know now that 15% of the gorilla genome is closer to humans than it is to chimps. Let's examine the totality of the evidence to get the complete picture, and not be so selective.

@Moo Moo: ERV insertion is not entirely random, but it isn't locus-specific either, even approximately. Relative to a particular locus, it's sufficiently random to make the probability of many independent ERV insertions at identical loci as close to zero as matters. And we are not speaking only of the several inserts that we share exclusively with the chimpanzee/bonobo clade, but also of many, many others that are orthologous between us and [hierarchically:] gorillas, all the great apes and gibbons, and all the Old World monkeys. Absolutely nothing except the pattern of relationships resulting from common ancestry comes anywhere close to explaining it all.

As Negative Entropy explained above, it's populations, not individuals, that diverge and speciate. A species may inherit genetic variants present already in its ancestor, and their displacement by other variants can be completed independently in different descendants. Incomplete resolution is thus not only possible but even expected for closely related taxa. You are right: it's indeed important to use the complete picture. What is the complete picture, then? Some of the evidence, when examined selectively, favours a closer relationship between Pan and Gorilla or Gorilla and Homo. But the total evidence makes it clear that chimps and humans cluster together to the exclusion of gorillas, who are nevertheless their closest living cousins.

@Piotr: Firtly, we don't know enough about retoviral insertion "hotspots" in order to make the sweeping generalization you have just made. The evidence suggests otherwise:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836564/

Moreover, chimps have over 100 copies of a virus called Pan troglodytes endogenous retrovirus(PtERV) and gorillas have about 80 copies. Humans have none. Now what does that say?

I should also point out that these ERV insertions are believed to happen in individuals and then get fixed in the population by way of random drift. However, if we sequenced more genomes from members of the same species, we might get a much better picture of what is really going on.

Firtly, we don't know enough about retoviral insertion "hotspots" in order to make the sweeping generalization you have just made. The evidence suggests otherwise:...

And, purely by chance, the pattern of insert-sharing reflects a nested hierarchy miraculosly mirroring that of independently established clades, right? If we share lots of insertions with all the Old World simians, why only a subset of them is shared exclusively with the great apes, and a subset of that subset only with gorillas and chimps, and a sub-sub-subset with chimps and bonobos alone? Plese tell me how you propose to explain this pattern. Or give me examples of human ERVs with orthologues in macaques and baboons but not in gibbons or the great apes.

Moreover, chimps have over 100 copies of a virus called Pan troglodytes endogenous retrovirus(PtERV) and gorillas have about 80 copies. Humans have none. Now what does that say?

It's one of those pieces of evidence already mentioned which could be used to argue for a Pan/Gorilla clade (excluding humans) if it were not isolated and if were a solid piece, which it isn't. The inserts in question are found in non-orthologous loci and everything points to independent retrovirus infections in different ape species some 4 Myr ago, after the Homo/Pan split. Why were proto-humans not affected? This is one likely reason:

The inserts in question are found in non-orthologous loci and everything points to independent retrovirus infections in different ape species

I try so hard to give the likes of Moo Moo the benefit of the doubt. But I bet that instead of thinking "shit, I did not pay enough attention, good to learn about coalescence, orthology, and lineage-specific insertions" this person will be back with more "challenges." I also bet that despite being shown ignorant, wrong, and superficial in the "reading" of literature, this Moo Moo character will be using the very same examples next time he/she enters a discussion on evolution and retroviral insertions. They have no intentions to learn anything. It's all about bullshitting their way around).

Notice that instead of acknowledging the mistake in ignoring population genetics and coalescence theory, Moo Moo hoped that you had not seen my comment. Once you showed that you had seen, and understood, that, Moo Moo just jumped to another "challenge" based on half-read and misunderstood literature.

I still thank Moo Moo, because now I have a couple of nice articles to discuss in my courses to make sure that my students have learned to read carefully and that they understand some pretty important concepts.

Once you showed that you had seen, and understood, that, Moo Moo just jumped to another "challenge" based on half-read and misunderstood literature.

PtERV is of course another red herring. But there is actually one good example of an ERV present in chimps and gorillas at orthologous loci, but not humans:http://medicine.yale.edu/labs/kidd/www/399.pdf

It can hardly be anything else than the theoretically expected occasional mismatch between the family tree of the three genera and that of a specific genome fragment. Note that it involves closely related taxa and (as far as I know) no other violation of the cladistic hierarchy by orthologous ERV has been found in haplorrhines so far. I suppose it can be safely predicted that if other examples exist (as they likely do), they will also involve close cousins and will be vastly outnumbered by ERVs conforming to the phylogenetic pattern. Hence my bet that Moo Moo will not be able to present any examples of orthologous ERVs present, say, in macaques and humans but sidestepping all the great apes and gibbons: to make it possible, an ancient polymorphism would have had to be maintained for unrealistically long (tens of millions of years). OTOH, Moo Moo's "favoured insertion locus" explanation does not prohibit any such thing. Quite the opposite -- it should be a common phenomenon. So where are the examples? ;)

"This is one of many posts comparing the understanding and interpretation of data on protein functions and evolution by scientists and creationists.

On one side there are thousands of protein chemists, biochemists, molecular biologists, cell biologists, evolutionists and many other scientists studding proteins. The scientists are supported by a huge academic and technical infrastructure worth billions of dollars. On the other side there are a few dozen people, if that, with very limited resources, if any."

Hi Claudiu, something to consider is that creationists also have a huge infrastructure worth billions of dollars. That infrastructure is all the churches and other religious groups/organizations on Earth, including all of their assets, holdings, investments, donations, etc.). On the whole, and even individually in many cases, creationists have and spend enormous amounts of money. They just don't spend much of it (if any) on scientific research (or at least on scientific research into evolution or the OOL).

The evolution and science bashing vocal creationists who pretend to be scientists or scientific groups/organizations (e.g. ICR, discovery institute, etc.) of course don't control or have access to all the money that creationists around the world have but they do have access to way more money than they're actually spending on scientific research. The majority of their money is spent on propaganda.

If the money that is spent by god pushers on stained glass alone were instead spent on scientific research or something else worthwhile, the world would be a better place.

Indeed, it would be remarkable to have some of the resources you mentioned directed at exploring issues of great significance, such as understanding protein evolution, the theme of this post. And, it would make sense to explore protein evolution in context of fields that are of extraordinary medical, public health and economic significance, such as the field of neurodegenerative diseases.

As I pointed out in my comment above, it is unconceivable that the scientists studying Alzheimer’s, Parkinson’s, Huntington’s, Creutzfeldt-Jakob disease, ALS and other neurodegenerative diseases have departed from one of the most fundamental scientific principles: "Nothing in Biology Makes Sense Except in the Light of Evolution.”

Circumventing this principle in order to cover up the potential scientific flaws of the ‘prion hypothesis’ and 'protein misfolding concept’, which have directed most of the thinking and research in these fields for decades, is a disservice not only to science, including evolution, but to tens of millions of patients and their families affected by these devastating diseases.

@Piotr:And, purely by chance, the pattern of insert-sharing reflects a nested hierarchy miraculosly mirroring that of independently established clades, right?

No. It reflects a common susceptibility to infection. You don't have to explain things in such extreme terms as that of a common ancestry and nested hierarchies.

Please tell me how you propose to explain this pattern.

Very simply, actually.

1. Chromosome structure. You would tend to expect that organisms with similar chromosomes would be more likely to have the same ERV insertions. Of course, you would try and explain shared chromosome structure in terms of common ancestry using circular logic.

2.Environment. Organisms living in the same environment tend to be at risk from the same infectious viruses. This helps explain why chimps and gorillas may have been infected with PtERV, but not humans.

Or give me examples of human ERVs with orthologues in macaques and baboons but not in gibbons or the great apes.

I'm sure if you look hard enough for them, you will find them. But do you really want to discover such "anomalies".

Chromosome structure. You would tend to expect that organisms with similar chromosomes would be more likely to have the same ERV insertions.

Why would they also have different ERV insertions that fail to mirror the cladistic pattern? (You have yourself provided an example). And yes, there is plenty of evidence from various areas pointing in the same direction -- common descent. The ERVs are just one type of evidence among many.

Of course, you would try and explain shared chromosome structure in terms of common ancestry using circular logic.

What is the creationist alternative?

2.Environment. Organisms living in the same environment tend to be at risk from the same infectious viruses. This helps explain why chimps and gorillas may have been infected with PtERV, but not humans.

Certainly, but PtERV is irrelevant, since it isn't even orthologous between the apes that have it. It's an example of a recent retrovirus incorporation, actually showing the difference between such a sevondary "similarity" and an ERV inherited from a common ancestor.

I'm sure if you look hard enough for them, you will find them. But do you really want to discover such "anomalies".

You should want to discover them, since they would falsify the standard explanation of the ERV occurrence pattern. I bet you won't find them, but go ahead, keep trying.

Moo Moo: You don't have to explain things in such extreme terms as that of a common ancestry and nested hierarchies.

Actually, I have to because common descent is the most parsimonious explanation of a whole big bundle of facts which would otherwise have to be explained ad hoc. I forgot to mention another such fact: that ERVs are the inactive and decomposing remains of the original proviruses, and that you can estimate the age of an ERV e.g. from the degree of divergence between its long terminal repeat sequences. And guess what? The more distant the phylogenetic relationship, the greater the divergence in orthologous ERVs. This correlation naturally falls out from common ancestry (reflecting the greater age of more inclusive clades).

What is the alternative? Did the Intelligent Designer deliberately insert mutations into the LTRs to make them appear older in more distantly related taxa? What for? To test the strength our faith by deceiving us? Or have you got more ad hoc stuff up your sleeve?

@Piotr: Your "parsimony" is quite subjective - it is just confirmation bias at work. No, DNA and mutations do not come with a timestamp. Degeneration can happen very rapidly or very slowly and there is no way one can tell. That's a poor argument for you to make.

I just gave you my alternative: common chromosomal structures and environmental factors both explain the shared ERV insertions, and also the differences between species, and individuals as well. You completely avoided the fact that both humans and chimps are likely to experience the same mutational and ERV hotspots on account of their overall chromosomal homology.

And you are wrong about common descent being falsifiable. If I found ERVs in macaques, orangutans, gorillas, bonobos and chimps, but not in humans, you would just say that somehow they were deleted from our genome.

Moo Moo: Your "parsimony" is quite subjective - it is just confirmation bias at work.

LOL. Several different kinds of evidence pointing in the same direction = confirmation bias. We would still believe in a flat earth if people had said that several different proofs independently confirming that the earth was round agreed because of a "confirmation bias".

No, DNA and mutations do not come with a timestamp. Degeneration can happen very rapidly or very slowly and there is no way one can tell. That's a poor argument for you to make.

A robust correlation is there for everyone to see. *Of course* there are complicating factors, *of course* trying to date a piece of DNA accurately using just one method is problematic, etc. etc. etc. But the fact remains: ERVs shared by more distantly related taxa are on the average more degraded.

I just gave you my alternative: common chromosomal structures and environmental factors both explain the shared ERV insertions, and also the differences between species, and individuals as well. You completely avoided the fact that both humans and chimps are likely to experience the same mutational and ERV hotspots on account of their overall chromosomal homology.

And the ERVs shared by humans and chimps but not other primates have far less divergent LTRs than those shared also by other primates.

And you are wrong about common descent being falsifiable. If I found ERVs in macaques, orangutans, gorillas, bonobos and chimps, but not in humans, you would just say that somehow they were deleted from our genome.

I gave you my idea of a test. It is completely different from what you say above. Your test would not falsify common descent -- mine would. Please read again what I wrote and try to understand it.

@Piotr: You are looking at a selected portion of the evidence and then confirming your own bias by examining it.

Here is a thought for you: Let us accept that ERVs shared between chickens and humans are more divergent in sequence than those between chimps and humans. Does that in itself indicate common ancestry between chickens and humans? I don't think that this necessarily follows at all. For one thing, the mutation and recombination rates, as well as hotspots, between chickens and humans are a lot different whereas they are similar for chimps and humans.

As for your example of shared ERVs between macaques and humans, but excluding gibbons and great apes, the same principle applies. If I found them in abundance, you would just retort by asserting that the ERVs somehow got separately deleted from the chimp and gorilla lineages. You can ,therefore, avoid falsification through speculation.

Here is a thought for you: Let us accept that ERVs shared between chickens and humans are more divergent in sequence than those between chimps and humans. Does that in itself indicate common ancestry between chickens and humans?

In itself? Hell, no. Cumulatively, with other evidence, yes. Shared origin, by the way, also explains why finding recognisable inherited ERVs in humans and chicken is extremely difficult if at all possible. They would have to go back more than 320 million years, which is long enough for ERV structure to erode away unless specially conserved for some reason.

I don't think that this necessarily follows at all. For one thing, the mutation and recombination rates, as well as hotspots, between chickens and humans are a lot different whereas they are similar for chimps and humans.

That's why we've been talking of a relatively young taxon (the Old World monkeys, including apes and humans). It's time depth is about 35 million years, about 10% of the age of the human/chicken LCA.

As for your example of shared ERVs between macaques and humans, but excluding gibbons and great apes, the same principle applies. If I found them in abundance, you would just retort by asserting that the ERVs somehow got separately deleted from the chimp and gorilla lineages. You can ,therefore, avoid falsification through speculation.

Can I? I'd have to say it was lost independently at least four times: in gibbons, orangs, gorillas, and chimps. That would be special pleading, and a real blow for the theory that orthologous ERVs can be used as evidence of common descent. Still, I abide by my prediction: there are no such ERVs, or at the very least their existence is *extremely* unlikely. In your explanation, however, nothing should stop them from occurring frequently. Where are they?

As for your example of shared ERVs between macaques and humans, but excluding gibbons and great apes, the same principle applies. If I found them in abundance, you would just retort by asserting that the ERVs somehow got separately deleted from the chimp and gorilla lineages

False. Population genetics and coalescence theory can only justify cases to a point. Make it better, find such things, then find cases that would make the picture even harder to maintain. Put the whole thing in context. Do the math. After you do that we talk. In the meantime you should learn the terms, the concepts and the math. Your ignorance is no justification to just continue with your bullshit. If you don't care then feel free to go fuck yourself. I often wonder why ass-holes like yourself feel so authoritative to challenge what they don't understand, and when shown to be ignorant continue as if nothing happened. It only comes to confirm that to be a creationist in the face of contradictory evidence you have to be an imbecile.

Moo Moo writes: Degeneration can happen very rapidly or very slowly and there is no way one can tell.

Oh, so the fact that degree of genetic difference corresponds to degree of relatedness reconstructed from the fossil record is sheer accident having nothing to do with more time having elapsed since species last shared a common ancestor?

So DNA evidence of relatedness within humans is utterly unreliable, since if there is no "clock," not even roughly, our genetic makeup might diverge as widely from our parents as it would from someone with whom we last shared an ancestor twenty or a thousand generations ago?

You'll be wanting to inform the courts of this, they're all laboring under a terrible misapprehension.

They would have to go back more than 320 million years, which is long enough for ERV structure to erode away unless specially conserved for some reason.

Well, many ERVs do play a role in gene regulation and are quite well conserved among taxa. Hence, we should take a look at chickens.

Can I? I'd have to say it was lost independently at least four times: in gibbons, orangs, gorillas, and chimps. That would be special pleading, and a real blow for the theory that orthologous ERVs can be used as evidence of common descent. Still, I abide by my prediction: there are no such ERVs, or at the very least their existence is *extremely* unlikely.

There is an alternative explanation you could use: parallel ERV evolution in macaques and humans for reasons we don't fully understand. That way there would be no loss in the other lineages. The only thing limiting an explanation is your own imagination - I have been told this many times by evolutionism apologists.

In your explanation, however, nothing should stop them from occurring frequently. Where are they?

We'll find them..it will just take some time. But, meanwhile, you might want to consider this: not only are ERV integration sites not random, but one also has to realize that ERV insertions in most regions are likely to prove deleterious. Hence, those ERV insertion sites that do exist in genomes may represent the few relatively "safe zones". This further undermines the significance of shared sites.

There is an alternative explanation you could use: parallel ERV evolution in macaques and humans for reasons we don't fully understand. That way there would be no loss in the other lineages. The only thing limiting an explanation is your own imagination - I have been told this many times by evolutionism apologists.

LMAO, now a straw man for a change, after red herrings. The fact is, there's already a perfectly good explanation of the patterns visible in the data and it's little use imagining what I would say if things were different. And the data are what they are: consistent with what we can predict assuming common descent.

We'll find them..it will just take some time.

Rubbish. Nothing you have said so far would have prevented any number of orthologous ERVs to sidestep any number of intermediate side branches in the cladogram any number of times. There should be *plenty* of such cases, given the huge number of primate ERVs recognised so far. The distribution of *all* those that we know follows the nested hierarchy with one sole exception where just one branch is skipped. That's as neat as can be.

Have a nice day, I've wasted enough time arguing that 2+2=4 when the opponent believes that arithmetic is a sin.

@Piotr: No, you're now avoiding the fact that there is no way to absolutely falsify common ancestry using something which does not fit in with your pattern of common ancestry (like PtERV insertions). It's because common ancestry can never be either observed or falsified based on DNA evidence alone.

The distribution of ERVs follows a pattern of common susceptibility, due to common chromosomal and environmental factors, and not common ancestry. The level of sequence divergence observed is readily explicable in terms of differences in mutation rates, hotspots and generation times. You're seeing a nested hierarchy when none need exist. Thanks for playing, but you lost the argument.

@Piotr: No, the PtERV insertions are orthologous to chimps and gorillas and, assuming common ancestry, they were thus inherited by the MRCA of chimps and gorillas.

But the most recent common ancestor of chimps and gorillas would also have been the MRCA of humans as well. Hence, it makes no sense for humans to be missing all of these insertions. But you avoid this potentially falsifying information by claiming one of two things:

1. The ERVs were mysteriously all deleted from the human lineage.

2. The ERVs independently infected the chimp and gorilla lineages.

Like I say, evolutionism is unfalsifiable. Your argument is worthless.

@Piotr: It is clear you are now getting increasingly desperate and exasperated as your argument collapses. 4% will do very nicely, thank you. If anything, it confirms that integration sites are non-random if the locality of the insertions is not based on common ancestry - so that destroys your previous assertion.

Let us read what the authors of the original research go on to say, shall we?

PTERV1 phylogenetic tree is inconsistent with the generally accepted species tree for primates....... An alternative explanation may be that the primate phylogeny is grossly incorrect, as has been proposed by a minority of anthropologists

Well, we told you so, didn't we? When you examine micro-RNAs, the grand phylogenetic inference also breaks down:

What 4%? You would have to prove first they are orthologous, which is neither demonstrated nor implied by the authors. The actual finding of the study is: 95.8% definitely non-homologous, the rest unmappable (NOT proven orthologous). You can read, can't you? so read the whole damn thing.

Quote:

"The number of non-orthologous loci was calculated as 275/287 (275+/-12) or 95.8%. This is almost certainly a lower-bound estimate owing to the limitation of our BAC-based mapping approach to refine the precise locations of the insertions."

Let us read what the authors of the original research go on to say, shall we?

By all means, read ON:

"This seems unlikely in light of the extensive molecular evolutionary data that have been collected over the last few years that clearly place orangutan as the outgroup species to the human–chimpanzee–gorilla clade and Old World monkeys as an outgroup to the human/ape lineage."

"We performed two analyses to determine whether these 12 shared map intervals might indeed be orthologous....only one interval is shared by gorilla and chimpanzee; however, two intervals are shared by gorilla and baboon; while three intervals are apparently shared by macaque and chimpanzee."

Oh dear! That is the exact opposite of what you would expect from the phylogenetic tree. Oh, look! More confirmation about what I was talking about before:

"This apparent independent clustering of retroviral insertions at similar locations may be a consequence of preferential integration bias or the effect of selection pressure against gene regions, limiting the number of effective sites that are tolerated for fixation."

Understand? There are *preferential integration sites* and there are also sites preferred by selection. This is *exactly* what I wrote previously. As such, the gorillas, chimps, orangs and baboons have all been independently infected but any overlap is due to deterministic factors of the kind that I also described previously.

@Moo Moo: You are the master of quote-mining. You skipped the part of the paragraph which confirms what I wrote, and quoted (and misinterpreted) just one sentence. Note that neither "shared intervals" nor "similar locations" means "identical loci". The sentence you quote is preceded by this:

"Although the status of the remaining overlapping sites is unknown, these data resolve four additional sites as independent insertion events and suggest that the remainder may similarly be non-orthologous."

So where the bloody hell are your alleged orthologous insertions? The study does not claim orthology for even one of them, and this is what I've been telling you all along.

@Jud: Er...no. "Preferred by selection" means that those ERVs that have integrated into the genome have done so only because the locations they inserted themselves into did not, as a consequence, produce a significant deleterious effect on reproductive fitness.

@Piotr: Orthologous insertions need not reside at identical locations. Why? I suggest you read this statement in the introduction of the paper:

Endogenous retroviruses may arise within genomes by at least two different mechanisms: retrotransposition from a pre-existing endogenous retrovirus (intraspecific transmission) or infection and integration via an exogenous source virus (horizontal transmission).

This means that ERVs can be copied and moved about while the original site can then be deleted. But, in any case, all this is just a red herring on your part because this study has established the following things:

1. There is a family of ERVs that clearly do not fit in with the common ancestry model of inherited variation.

2. ERV nsertions may be restricted in location to preferential integration sites and are further restricted by natural selection due to their effect on fitness.

3. It is not possible to falsify common ancestry because independent insertion and deletion can account for any anomalies.

Hence, there is no need to suppose common ancestry as the only possible explanation when accounting for shared ERVs.

1. The vast majority of all ERV insertions in Catarrhini are orthologous (the ratio of non-orthologous to orthologous insertions is about 0.1%)

2. Practically all orthologous insertions (with a single known exception) conform to the nested hierachy of common descent. The one exception (HERV-K-GC1) deviates from the hierarchy at just one point, which is perfectly consistent with the mechanism of allelic segregation.

3. There may also be deviations due to the non-random character of ERV insertion (at preferred target sites). These may produce "pseudoorthologies" if retroviruses independently reuse identical sites. The few studies that have tried to estimate the frequency of such events based on the observed behaviour of retroviruses suggest that they are rare, accounting for maybe some 0.1% of all endogenous retroviral placements. Hardly enough to undermine anything.

4. Unambigously non-orthologous insertions are simply irrelevant. If they don't conform to the nested hierarchy, it does no harm to the model, since nobody expects them to fit in.

Moo Moo writes: "Preferred by selection" means that those ERVs that have integrated into the genome have done so only because the locations they inserted themselves into did not, as a consequence, produce a significant deleterious effect on reproductive fitness.

Are you really this dense, or only pretemding? Reproductive fitness. Resulting in heirs in the direction forward in time, ancestors in the direction back in time. Thus not independent.

The only way to determine reproductive fitness is to compare the species around today to others current and past. The pattern is quite clear that those we would expect by the fossil record to be more closely related show up as more closely related through DNA. One might contend, as you do, that this is a vanishingly unlikely series of independent occurrences (something like ignoring footprints leading into a house, to a room where a person lies dead of gunshot, then back out of the house, and concluding the death was by suicide); or the caprice of a Designer with an antic sense of humor, who wishes to align DNA with the fossil record when there is no necessity to do so; or one might go where the evidence points so very strongly, which is that the elementary basis for alignment of the fossil record with DNA is the relation of species through common ancestry.

Time for a rethink."hahaha no:http://m.gbe.oxfordjournals.org/content/5/5/819.fullhttp://dx.doi.org/10.1098/rsbl.2012.0331Second the man hasn't published his results which is a big red flag, third there is such a convergence of evidence from so many other fields that an alternate sequence

Moo moo also says "2. ERV nsertions may be restricted in location to preferential integration sites and are further restricted by natural selection due to their effect on fitness."Hahaha no: "Just as with the other examples, rather than demonstrating locus specificity, what is actually being demonstrated is the ability to insert anywhere in the genome, as well as certain areas of higher and lower frequency of insertions, i.e. target site preference.

This is clearly illustrated throughout source the Sverdlov (1998) paper itself (yes, 1998; read the aside) gets the information in the quote from; as the following quotations show:

In this report we extend the PCR-based approach to examine integration within chromosomal targets in vivo. These studies were initiated to test and extend our previous work on the specificity of ALV integration into cell DNA (Shih et al. 1988). For this purpose, we developed a system that detects single integration events in a population of cells at any defined genomic site with single nucleotide resolution. Using this approach we have found that all regions of the genome examined were accessible to retroviral integration. Localized preferences were seen within regions, with some sites being used up to 280 times greater than random (Withers-Ward et al., 1914, p. 1474).

Figure 5 is a graphic presentation summarizing all of the integration events detected within four preselected and two unselected regions. Integrations were detected throughout the sequence in each region with localized hyperreactive sites that were used at a frequency up to 280-fold greater than random. No obvious distinction could be made between sites selected on the basis of previous integration and those chosen at random (Withers-Ward et al., 1914, p. 1477).

[emphasis added]

An even more striking example comes from Wang et al. (2007), where an unprecedented “40,569 unique integration site sequences” were analyzed. Of all those integration events, only 41 “hosted two independent integration events at exactly the same base pair in the human genome (Wang et al., 2007, p. 1188).” Again, shared insertions resulting from parallel integration is rare—not as rare as so many misinformed individuals on the internet that use the ERV argument claim—but rare enough to make it unambiguously clear that retroviral insertion is not locus specific." http://m.evolutionarymodel.com/site/mobile?dm_path=%2Fervs.htm&fw_sig_site=47462214&fw_sig_session_key=20317effd710706eae7cf9aad251745403e724021413aa08229417628ec1af00-47462214&fw_sig_is_admin=0&fw_sig_partner=webs&fw_sig_permissions=none&fw_sig_url=http://www.evolutionarymodel.com/&fw_sig=80bcc970991427182acf39e41b8d271f&fw_sig_tier=0&fw_sig_api_key=522b0eedffc137c934fc7268582d53a1&fw_sig_time=1430920899958&fw_sig_potential_abuse=1&fw_sig_social=1&fw_sig_locale=en-US&fw_sig_access_token=748224af048e640a92bbde17489bfa77ce7051d7&fw_sig_permission_level=0&fw_sig_premium=1&fb_sig_network=fw#1320

That's why we've been talking of a relatively young taxon (the Old World monkeys, including apes and humans). It's time depth is about 35 million years, about 10% of the age of the human/chicken LCA.

Not to mention that macaques have shorter generation spans than humans and chimps; hence I one would expect their genome, including any ERV integration sites, to be more divergent.

All of this does not detract from my original point which is that there exists no fossil evidence of any human-chimp CA, nor of a gorilla-human-chimp CA, nor one for the great apes, nor one for the great and lesser apes, nor one for Old World monkeys. That is remarkable evidence against common ancestry. The only excuse I hear is that the "dog ate my homework" on account of the acidic forest soil.

@whole truth: No, I presume that the common ancestral *species/population* of humans and chimps was around long enough for this to be observed in the fossil record. But no such evidence exists despite the abundance of primate fossils in East Africa. Absence of evidence, in this case, is evidence of absence.

moo moo, you're presuming many other things too. I'd point them all out but I have better things to do and I suggest that you just go to Africa and help the small number of people who are searching for primate fossils. After a few days, if not sooner, you'll start to understand how difficult it is to search such a vast, rugged continent and all the factors involved in such fossils forming in the first place and then surviving millions of years of crushing burial, weathering, flooding (including burial under more and more sediments), erosion, damage or destruction by plant roots, gnawing by rodents, fires, volcanic activity, animal trampling, earthquakes, landslides, etc., and you'll also discover that such fossils are really, really unlikely to be lying around on the surface in plain view and in good condition for you or someone else to easily find.

Besides, if or when fossils are found that are said by scientists to be from the direct common ancestor of human and chimps, will you accept it?

@the whole truth: Poppycock. You are just claiming that the "dog ate my homework". We have uncovered lots of primate fossils, yet none of the putative common ancestral species of the various families and sub-families of the order.

If someone claims to have dug the MRCA up, I will definitely consider the evidence presented - although I suspect it will be another "Ida". You should know that many species thought to be in the evolutionary lineage of humans, like "Homo habilis" and also "Australopithecus afarensis" are no longer considered to be direct ancestors.

You should know that many species thought to be in the evolutionary lineage of humans, like "Homo habilis" and also "Australopithecus afarensis" are no longer considered to be direct ancestors.

Piotr,That sentence is clear evidence that this Moo Moo is too much of an ass-hole. Not understanding the relationships expected between fossilized organisms and present-day ones. I suspect that this idiot just wants to figure out how much she/he can have you to answer (pure trolling strategy). Take a look, this ass-hole makes it too easy to spot the many mistakes she/he makes. Notice the style in the answers, classic troll rhetoric: "4% will do," "you avoided this," "time for a rethink" ...

"Poppycock. You are just claiming that the "dog ate my homework". We have uncovered lots of primate fossils, yet none of the putative common ancestral species of the various families and sub-families of the order."

You apparently think that everything that ever lived on this planet must have left plenty of fossils, and that if those fossils haven't been found yet they never will be, therefor those things must not have ever lived, therefor god-jesus and special creation.

You must think that all fossils should be common and easy to find and that all prehistoric primates and all other living things were dropping dead in all the right places just so that someone could come along millions of years later and easily find their well preserved fossilized parts. If so, your lack of knowledge regarding fossils is profound.

And even if all of the continent of Africa right down to the basement rock were put through a fine-mesh screen today and no fossils were found of THE direct human/chimp ancestor, it wouldn't prove that no such ancestor ever lived. It would only prove that no fossils of that ancestor currently exist in the continent of Africa, and since no one is going to put the entire continent through a screen today it's premature to assume that no such fossils will ever be found.

New to science, 'gap' filling fossils are regularly found of various life forms, including primates at times. Be patient, you never know what tomorrow may bring.

Is there any fossil evidence of yhwh, satan, adam, eve, cain, abel, jesus, moses, jonah, or noah and his wife and children? If not, that is remarkable evidence against their existence and your descent from whichever one(s) you may think you're descended from or were created by.

Is there any fossil evidence of your alleged great, great, great, great, great, great, great, great, great, great, great, great, great grandfather and grandmother? If not, that is remarkable evidence against their existence and your descent from them.

This post just shows that you're not even aware of what ID advocates are claiming. ID and common ancestry are compatible, though admittedly many IDers do not believe in common ancestry though I do to a limited extent. Common ancestry is not the issue, it's natural selection acting on random mutations that is at issue. As far as Cain, Abel, etc, ID takes no stand on Christianity or the Bible which in my mind are untrue anyway. If you read L Moran's post what he does not tell you is that there is not one step by step description of how one protein changed into another protein for which the amino acid sequence is different by a factor of around 3%. That should disturb you. There is no evidence for NS acting on RM and I challenge you to find some. There are 600 genes not shared by chimps and humans. Give me an account of how 1 of those genes arose through NS acting on RM.

When a new species is designed the unconscious mind of the organism intentionally manipulates the genetic code. We humans have the ability to move matter (we would not be able to impose our will on nature if it were not the case) it is reasonable therefore to conclude that we can also move the matter that makes up our DNA.

ID and common ancestry are compatible, though admittedly many IDers do not believe in common ancestry

If they can't agree on this, then how are they supposed to be able to find actual signs of design and differentiate them from signs of common ancestry? If they can't use the evidence and solve this "internal problem" they should not be talking about an intelligent design theory. Do you see the huge problem this signifies at all?

there is not one step by step description of how one protein changed into another protein for which the amino acid sequence is different by a factor of around 3%

Those who have studied evolution have found clear and natural explanations for step-by-step changes in proteins differing by more than 45% in amino-acid sequence. I see no reason to be disturbed because some creationists who can't put their own act together go searching for whatever example of protein evolution that has not been studied, present that (ignoring what we actually know) to their followers and conclude: "therefore magic."

There is no evidence for NS acting on RM and I challenge you to find some

Actually there's tons of evidence for NS acting on RM. This is why even YECs (the most irrational among creationists) accept this to happen only to reject that it is able to go beyond "kinds."

There are 600 genes not shared by chimps and humans

How interesting. Did you check this out yourself or did you buy it from some other IDiot? Did you go check which genes could these be and perhaps whether they look, or not, as if they appeared by magic? For example, I know that there's lots of viral insertions in chimps that do not appear in humans. They have a perfectly clear and natural explanation. We have viral insertions that chimps don't. They have a perfectly clear and natural explanation. We check those things carefully. You just look at abstracts and IDiot claims, but do you look at the data? I doubt it. All your claims are clearly shallow in understanding, in thinking, and in every other possible way. You are just an ass-hole parroting what you hear from other IDIots.

Forgive my ignorance, I am not scientist but just trying to understand this better. Does the author imply in the article above that the common ancestor to apes and chimps lived "hundreds of millions of years ago"?

"Changing one of the modern enzymes into the other would require many changes because in most cases the common ancestor dates back hundreds of millions of years."

I have seen references to this in the posts above also. It was my understanding that the asteroid impact 65 million years ago wiped out most, if not all, life on the planet including the dinosaurs. If that is the case would not all life on the planet today have evolved from what was left in just 65 million years?

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.